PyCogent 10: basic DNA methods

I'm exploring PyCogent (docs, download page)---first post here.

We'll use this method from the last post (and you'll also need to load the data from your favorite FASTA-formatted sequence file), as shown in that example.

from cogent import Sequence, DNA # method 1: from a string seq = Sequence(moltype=DNA, name=n, seq=s) print '1', seq[:24] print type(seq) print seq[:36].toFasta()

<class 'cogent.core.sequence.DnaSequence'> >SThemA ATGACCCTTTTAGCGCTCGGTATTAACCATAAAACG

print seq.Name print seq[:36] print seq[:36].complement() print seq.MW() # this strand only

SThemA ATGACCCTTTTAGCGCTCGGTATTAACCATAAAACG TACTGGGAAAATCGCGAGCCATAATTGGTATTTTGC 365443.89

print seq[:36].rc() # reverse complement print seq.canPair(seq.rc())

CGTTTTATGGTTAATACCGAGCGCTAAAAGGGTCAT True

print seq[-36:].toRna() print seq.hasTerminalStop()

CUGAAUAUUCUGCGCGACAGCCUCGGGCUGGAGUAG True

s = seq.withoutTerminalStopCodon() print s[-33:] print s.getTranslation()[-11:] print s.getOrfPositions()

CTGAATATTCTGCGCGACAGCCTCGGGCTGGAG LNILRDSLGLE [(0, 1254)]

s = seq.toFasta().split('\n',1)[1] print s[:36] print type(s)

ATGACCCTTTTAGCGCTCGGTATTAACCATAAAACG <type 'str'>

mseq = seq.shuffle() print seq[:36] print mseq[:36] print seq.count('g') == mseq.count('g') print all([seq.count(n) == mseq.count(n) for n in 'acgt'])

ATGACCCTTTTAGCGCTCGGTATTAACCATAAAACG GGTCCAATGTCCCAGCGACTGAGCTGTGAACGTTAA True True